Contacts of the strand formed by residues 1813 - 1817 (chain A) in PDB entry 2V5P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR1813 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1806A LEU 3.8 6.2 - - - +
1807A THR* 4.3 7.2 - - - -
1811A LEU* 3.1 71.2 + - + +
1812A LEU* 1.3 79.5 + - - +
1814A SER* 1.3 70.4 + - - +
1815A PHE* 3.7 22.0 - + - -
1876A TYR* 5.5 1.9 + - - -
1987A CYS 4.5 2.9 + - - -
1988A PRO 4.0 19.4 + - - -
1989A PRO* 4.0 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1814 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1805A THR* 4.7 14.5 - - - +
1806A LEU 3.1 13.2 - - - -
1807A THR* 4.8 7.0 - - - -
1813A TYR* 1.3 85.5 - - - +
1815A PHE* 1.3 64.8 + - - +
1816A ASN* 4.0 2.8 + - - +
1E NAG 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1815 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1805A THR* 3.3 7.0 - - - -
1806A LEU* 3.2 50.7 + - + -
1811A LEU* 3.5 25.6 - - + -
1813A TYR* 3.7 25.1 - + - -
1814A SER* 1.3 75.6 - - - +
1816A ASN* 1.3 59.7 - - - +
1817A LEU* 3.3 12.9 + - + +
1876A TYR* 4.0 18.4 - + - -
1883A VAL* 3.9 12.1 - - + -
1985A VAL* 3.4 18.6 - - + +
1986A VAL* 3.6 20.4 - - + -
1987A CYS 3.5 30.7 - - - -
1988A PRO* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1816 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1805A THR* 3.6 14.2 - - + +
1814A SER* 4.0 4.1 + - - +
1815A PHE* 1.3 68.0 - - - +
1817A LEU* 1.3 60.1 + - - +
1818A SER* 3.3 17.1 + - - -
1819A SER* 3.5 10.2 + - - -
1985A VAL* 3.1 24.0 + - + +
1E NAG 1.4 68.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1817 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1804A CYS* 3.3 25.8 + - - +
1806A LEU* 5.3 0.9 - - + -
1815A PHE* 3.3 12.6 + - + +
1816A ASN* 1.3 68.8 - - - +
1818A SER* 1.3 57.7 + - - +
1819A SER* 3.1 3.6 - - - -
1820A LEU* 3.1 31.9 + - + +
1821A SER 3.6 3.6 + - - -
1838A VAL* 4.2 9.9 - - + +
1872A MET* 5.2 2.5 - - + -
1874A LEU* 3.8 40.8 - - + -
1883A VAL* 4.3 10.3 - - + -
1885A LEU* 5.6 0.2 - - + -
1955A PHE* 4.3 29.4 - - + -
1983A THR* 5.8 0.2 - - - +
1985A VAL* 4.5 9.9 - - + -
1986A VAL* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il